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. 2009 Dec 24;5(12):e1000597. doi: 10.1371/journal.pcbi.1000597

Figure 2. Example of text-mined PPI network.

Figure 2

The nodes are proteins identified using the query: “leukoencephalopathy, progressive multifocal”[mh] antibody[pubmed] in GoGene [22]. The query retrieves gene symbols mapped to PubMed abstracts that include the keyword antibody and the MeSH term leukoencephalopathy, progressive multifocal (PML). The gene list was exported to SIF format and the gene symbols extracted and used to query PPI using iHOP Web services [69]. Only those iHOP interactions with at least two co-occurrences and confidence above zero were considered. The network was plotted using Cytoscape [70]. The node color is based on the number of interactions (node degree).